add charge failure

[chimerax-bug-report@…]

The following bug report has been submitted:
Platform:        Windows-10-10.0.19043
ChimeraX Version: 1.3rc202110272149 (2021-10-27 21:49:02 UTC)
Description
(Describe the actions that caused this problem to occur here)

Log:
UCSF ChimeraX version: 1.3rc202110272149 (2021-10-27)  
© 2016-2021 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

open E:/Projects/MoS2/Exfoliation/WithPeptide/output/stripped-
pep-1-100ns.xtc

No atomic models open to read the coordinates into!  

open E:/Projects/MoS2/Exfoliation/WithPeptide/output/stripped-
pep-1-100ns-195.gro

Cannot guess atomic element from atom name in file stripped-
pep-1-100ns-195.gro.  
Line: 8MSF MMS1 1255 3.345 3.452 0.823  

open E:/Projects/MoS2/Exfoliation/WithPeptide/output/stripped-
pep-1-100ns-195.gro

Cannot guess atomic element from atom name in file stripped-
pep-1-100ns-195.gro.  
Line: 8MSF MMS1 1255 3.345 3.452 0.823  

open E:/Projects/MoS2/Exfoliation/WithPeptide/output/stripped-
pep-1-100ns-1034.pdb

Summary of feedback from opening
E:/Projects/MoS2/Exfoliation/WithPeptide/output/stripped-pep-1-100ns-1034.pdb  
---  
warnings | Ignored bad PDB record found on line 1  
REMARK GENERATED BY TRJCONV  

Ignored bad PDB record found on line 3  
REMARK THIS IS A SIMULATION BOX  

stripped-pep-1-100ns-1034.pdb title:  
Protein + water t= 1030.00000 step= 1030000 [more info...]  

Chain information for stripped-pep-1-100ns-1034.pdb #1  
---  
Chain | Description  
A B C D E F G H I J K | No description available  

Non-standard residues in stripped-pep-1-100ns-1034.pdb #1  
---  
MS1 — (MS1)  
MS2 — (MS2)  
MSF — (MSF)  
MST — (MST)  


open E:/Projects/MoS2/Exfoliation/WithPeptide/output/stripped-
pep-1-100ns.xtc

Replaced existing frames of stripped-pep-1-100ns-1034.pdb #1 with 1026 new
frames  

hide surfaces

[Repeated 1 time(s)]

select protein

1254 atoms, 1276 bonds, 77 residues, 1 model selected  

hide sel surfaces

hide sel cartoons

show sel cartoons

show sel atoms

hide sel atoms

show sel atoms

hide sel surfaces

volume hide

No volumes specified  

show sel atoms

hide sel atoms

show sel atoms

hide sel atoms

select #1

11214 atoms, 1276 bonds, 87 residues, 1 model selected  

~select #1

Nothing selected  

lighting simple

lighting soft

lighting full

lighting simple

color #1 #00007f

lighting simple

set bgColor white

set bgColor gray

set bgColor black

set bgColor gray

set bgColor white

set bgColor gray

lighting full

lighting soft

lighting simple

view

graphics silhouettes true

view

lighting shadows true

lighting flat

lighting full

lighting soft

lighting simple

volume hide

No volumes specified  

show surfaces

hide surfaces

show cartoons

hide cartoons

[Repeated 1 time(s)]

show cartoons

hide cartoons

show atoms

hide cartoons

hide atoms

show atoms

hide cartoons

show cartoons

hide cartoons

show cartoons

select protein

1254 atoms, 1276 bonds, 77 residues, 1 model selected  

hide sel atoms

show sel cartoons

style sel stick

Changed 1254 atom styles  

style sel ball

Changed 1254 atom styles  

show sel atoms

style sel sphere

Changed 1254 atom styles  

style sel ball

Changed 1254 atom styles  

style sel stick

Changed 1254 atom styles  

hide sel atoms

rainbow sel

color sel byhetero

color sel bychain

color sel bypolymer

rainbow sel

coulombic sel

The following residues are missing heavy (non-hydrogen) atoms, which may
result in inaccurate electrostatics:  
/A TYR 7  
/B TYR 7  
/C TYR 7  
/D TYR 7  
/E TYR 7  
/F TYR 7  
/G TYR 7  
/H TYR 7  
/I TYR 7  
/J TYR 7  
/K TYR 7  

Using Amber 20 recommended default charges and atom types for standard
residues  
Nonstandard name for heavy atom /B TYR 7 OT2  

select : MSF MS1 MS2 MST

Expected a keyword  

select : MSF

996 atoms, 1 residue, 1 model selected  

select add : MS1 & MS2

Expected a keyword  

select add : MS1

4980 atoms, 5 residues, 1 model selected  

select : MST

996 atoms, 1 residue, 1 model selected  

select : MST and MS1

Expected a keyword  

select : MST, MS1

4980 atoms, 5 residues, 1 model selected  

select : MST, MS1, MST

4980 atoms, 5 residues, 1 model selected  

select : MST, MS1, MSF

5976 atoms, 6 residues, 1 model selected  

style sel stick

Changed 5976 atom styles  

style sel sphere

Changed 5976 atom styles  

select : MST, MS1, MSF, MS2

9960 atoms, 10 residues, 1 model selected  

show sel atoms

hide sel atoms

style sel stick

Changed 9960 atom styles  

style sel sphere

Changed 9960 atom styles  

show sel atoms

style sel ball

Changed 9960 atom styles  

style sel sphere

Changed 9960 atom styles  

lighting simple

ui tool show "Selection Inspector"

nucleotides sel atoms

style nucleic & sel stick

Changed 0 atom styles  

rainbow sel

color sel byhetero

[Repeated 1 time(s)]

color sel bychain

color sel bypolymer

rainbow sel

coulombic sel

Using Amber 20 recommended default charges and atom types for standard
residues  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.3rc\bin\lib\site-
packages\chimerax\toolbar\tool.py", line 205, in callback  
bundle_info.run_provider(session, name, session.toolbar,
display_name=display_name)  
File "C:\Program Files\ChimeraX 1.3rc\bin\lib\site-
packages\chimerax\core\toolshed\info.py", line 381, in run_provider  
return api._api_caller.run_provider(api, session, name, mgr, **kw)  
File "C:\Program Files\ChimeraX 1.3rc\bin\lib\site-
packages\chimerax\core\toolshed\\__init__.py", line 1283, in run_provider  
return cls._get_func(api, "run_provider")(session, name, mgr, **kw)  
File "C:\Program Files\ChimeraX 1.3rc\bin\lib\site-
packages\chimerax\shortcuts\\__init__.py", line 52, in run_provider  
shortcuts.run_provider(session, name)  
File "C:\Program Files\ChimeraX 1.3rc\bin\lib\site-
packages\chimerax\shortcuts\shortcuts.py", line 1334, in run_provider  
keyboard_shortcuts(session).try_shortcut(name)  
File "C:\Program Files\ChimeraX 1.3rc\bin\lib\site-
packages\chimerax\shortcuts\shortcuts.py", line 390, in try_shortcut  
self.run_shortcut(keys)  
File "C:\Program Files\ChimeraX 1.3rc\bin\lib\site-
packages\chimerax\shortcuts\shortcuts.py", line 408, in run_shortcut  
sc.run(self.session, status = self._enabled)  
File "C:\Program Files\ChimeraX 1.3rc\bin\lib\site-
packages\chimerax\shortcuts\shortcuts.py", line 327, in run  
f(s)  
File "C:\Program Files\ChimeraX 1.3rc\bin\lib\site-
packages\chimerax\shortcuts\shortcuts.py", line 61, in func_plus_tip  
func(cmd + " %s")(session)  
File "C:\Program Files\ChimeraX 1.3rc\bin\lib\site-
packages\chimerax\shortcuts\shortcuts.py", line 569, in run_expanded_command  
run(session, cmd)  
File "C:\Program Files\ChimeraX 1.3rc\bin\lib\site-
packages\chimerax\shortcuts\shortcuts.py", line 512, in run  
run_command(session, command, **kw)  
File "C:\Program Files\ChimeraX 1.3rc\bin\lib\site-
packages\chimerax\core\commands\run.py", line 36, in run  
results = command.run(text, log=log, return_json=return_json)  
File "C:\Program Files\ChimeraX 1.3rc\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2856, in run  
result = ci.function(session, **kw_args)  
File "C:\Program Files\ChimeraX 1.3rc\bin\lib\site-
packages\chimerax\coulombic\cmd.py", line 90, in cmd_coulombic  
assign_charges(session, needs_assignment, his_scheme, charge_method,  
File "C:\Program Files\ChimeraX 1.3rc\bin\lib\site-
packages\chimerax\coulombic\coulombic.py", line 95, in assign_charges  
add_charges(session, charged_residues, method=charge_method, status=status,  
File "C:\Program Files\ChimeraX 1.3rc\bin\lib\site-
packages\chimerax\add_charge\charge.py", line 23, in add_charges  
uncharged_res_types = add_standard_charges(session, residues, status=status,
query_user=query_user,  
File "C:\Program Files\ChimeraX 1.3rc\bin\lib\site-
packages\chimerax\add_charge\charge.py", line 233, in add_standard_charges  
del uncharged_res_types[res_type]  
KeyError: 'MSF[1MMS]'  

KeyError: 'MSF[1MMS]'  

File "C:\Program Files\ChimeraX 1.3rc\bin\lib\site-
packages\chimerax\add_charge\charge.py", line 233, in add_standard_charges  
del uncharged_res_types[res_type]  

See log for complete Python traceback.  


mlp sel

mlp: no amino acids specified  




OpenGL version: 3.3.13596 Core Profile Forward-Compatible Context 20.10.44 27.20.11044.7
OpenGL renderer: AMD Radeon(TM) Vega 8 Graphics
OpenGL vendor: ATI Technologies Inc.
Manufacturer: HP
Model: HP ENVY x360 Convertible 15-ds0xxx
OS: Microsoft Windows 10 Home (Build 19043)
Memory: 14,900,236,288
MaxProcessMemory: 137,438,953,344
CPU: 8 AMD Ryzen 5 3500U with Radeon Vega Mobile Gfx  
OSLanguage: en-US
Locale: ('en_US', 'cp1252')
PyQt5 5.15.2, Qt 5.15.2
Installed Packages:
   alabaster: 0.7.12
   appdirs: 1.4.4
   Babel: 2.9.1
   backcall: 0.2.0
   blockdiag: 2.0.1
   certifi: 2021.10.8
   cftime: 1.5.1
   charset-normalizer: 2.0.7
   ChimeraX-AddCharge: 1.1.4
   ChimeraX-AddH: 2.1.10
   ChimeraX-AlignmentAlgorithms: 2.0
   ChimeraX-AlignmentHdrs: 3.2
   ChimeraX-AlignmentMatrices: 2.0
   ChimeraX-Alignments: 2.2.3
   ChimeraX-AlphaFold: 1.0
   ChimeraX-AltlocExplorer: 1.0.1
   ChimeraX-AmberInfo: 1.0
   ChimeraX-Arrays: 1.0
   ChimeraX-Atomic: 1.30.2
   ChimeraX-AtomicLibrary: 4.1.5
   ChimeraX-AtomSearch: 2.0
   ChimeraX-AtomSearchLibrary: 1.0
   ChimeraX-AxesPlanes: 2.0
   ChimeraX-BasicActions: 1.1
   ChimeraX-BILD: 1.0
   ChimeraX-BlastProtein: 2.0
   ChimeraX-BondRot: 2.0
   ChimeraX-BugReporter: 1.0
   ChimeraX-BuildStructure: 2.6
   ChimeraX-Bumps: 1.0
   ChimeraX-BundleBuilder: 1.1
   ChimeraX-ButtonPanel: 1.0
   ChimeraX-CageBuilder: 1.0
   ChimeraX-CellPack: 1.0
   ChimeraX-Centroids: 1.2
   ChimeraX-ChemGroup: 2.0
   ChimeraX-Clashes: 2.2.2
   ChimeraX-ColorActions: 1.0
   ChimeraX-ColorGlobe: 1.0
   ChimeraX-ColorKey: 1.5
   ChimeraX-CommandLine: 1.1.5
   ChimeraX-ConnectStructure: 2.0
   ChimeraX-Contacts: 1.0
   ChimeraX-Core: 1.3rc202110272149
   ChimeraX-CoreFormats: 1.1
   ChimeraX-coulombic: 1.3.1
   ChimeraX-Crosslinks: 1.0
   ChimeraX-Crystal: 1.0
   ChimeraX-CrystalContacts: 1.0
   ChimeraX-DataFormats: 1.2.2
   ChimeraX-Dicom: 1.0
   ChimeraX-DistMonitor: 1.1.5
   ChimeraX-DistUI: 1.0
   ChimeraX-Dssp: 2.0
   ChimeraX-EMDB-SFF: 1.0
   ChimeraX-ExperimentalCommands: 1.0
   ChimeraX-FileHistory: 1.0
   ChimeraX-FunctionKey: 1.0
   ChimeraX-Geometry: 1.1
   ChimeraX-gltf: 1.0
   ChimeraX-Graphics: 1.1
   ChimeraX-Hbonds: 2.1.2
   ChimeraX-Help: 1.2
   ChimeraX-HKCage: 1.3
   ChimeraX-IHM: 1.1
   ChimeraX-ImageFormats: 1.2
   ChimeraX-IMOD: 1.0
   ChimeraX-IO: 1.0.1
   ChimeraX-ItemsInspection: 1.0
   ChimeraX-Label: 1.1
   ChimeraX-ListInfo: 1.1.1
   ChimeraX-Log: 1.1.4
   ChimeraX-LookingGlass: 1.1
   ChimeraX-Maestro: 1.8.1
   ChimeraX-Map: 1.1
   ChimeraX-MapData: 2.0
   ChimeraX-MapEraser: 1.0
   ChimeraX-MapFilter: 2.0
   ChimeraX-MapFit: 2.0
   ChimeraX-MapSeries: 2.1
   ChimeraX-Markers: 1.0
   ChimeraX-Mask: 1.0
   ChimeraX-MatchMaker: 2.0.2
   ChimeraX-MDcrds: 2.6
   ChimeraX-MedicalToolbar: 1.0.1
   ChimeraX-Meeting: 1.0
   ChimeraX-MLP: 1.1
   ChimeraX-mmCIF: 2.4
   ChimeraX-MMTF: 2.1
   ChimeraX-Modeller: 1.2.4
   ChimeraX-ModelPanel: 1.2
   ChimeraX-ModelSeries: 1.0
   ChimeraX-Mol2: 2.0
   ChimeraX-Morph: 1.0
   ChimeraX-MouseModes: 1.1
   ChimeraX-Movie: 1.0
   ChimeraX-Neuron: 1.0
   ChimeraX-Nucleotides: 2.0.2
   ChimeraX-OpenCommand: 1.7
   ChimeraX-PDB: 2.6.5
   ChimeraX-PDBBio: 1.0
   ChimeraX-PDBLibrary: 1.0.2
   ChimeraX-PDBMatrices: 1.0
   ChimeraX-PickBlobs: 1.0
   ChimeraX-Positions: 1.0
   ChimeraX-PresetMgr: 1.0.1
   ChimeraX-PubChem: 2.1
   ChimeraX-ReadPbonds: 1.0
   ChimeraX-Registration: 1.1
   ChimeraX-RemoteControl: 1.0
   ChimeraX-ResidueFit: 1.0
   ChimeraX-RestServer: 1.1
   ChimeraX-RNALayout: 1.0
   ChimeraX-RotamerLibMgr: 2.0
   ChimeraX-RotamerLibsDunbrack: 2.0
   ChimeraX-RotamerLibsDynameomics: 2.0
   ChimeraX-RotamerLibsRichardson: 2.0
   ChimeraX-SaveCommand: 1.5
   ChimeraX-SchemeMgr: 1.0
   ChimeraX-SDF: 2.0
   ChimeraX-Segger: 1.0
   ChimeraX-Segment: 1.0
   ChimeraX-SelInspector: 1.0
   ChimeraX-SeqView: 2.4.5
   ChimeraX-Shape: 1.0.1
   ChimeraX-Shell: 1.0
   ChimeraX-Shortcuts: 1.1
   ChimeraX-ShowAttr: 1.0
   ChimeraX-ShowSequences: 1.0
   ChimeraX-SideView: 1.0
   ChimeraX-Smiles: 2.1
   ChimeraX-SmoothLines: 1.0
   ChimeraX-SpaceNavigator: 1.0
   ChimeraX-StdCommands: 1.6
   ChimeraX-STL: 1.0
   ChimeraX-Storm: 1.0
   ChimeraX-Struts: 1.0
   ChimeraX-Surface: 1.0
   ChimeraX-SwapAA: 2.0
   ChimeraX-SwapRes: 2.1
   ChimeraX-TapeMeasure: 1.0
   ChimeraX-Test: 1.0
   ChimeraX-Toolbar: 1.1
   ChimeraX-ToolshedUtils: 1.2
   ChimeraX-Tug: 1.0
   ChimeraX-UI: 1.13.7
   ChimeraX-uniprot: 2.2
   ChimeraX-UnitCell: 1.0
   ChimeraX-ViewDockX: 1.0.1
   ChimeraX-VIPERdb: 1.0
   ChimeraX-Vive: 1.1
   ChimeraX-VolumeMenu: 1.0
   ChimeraX-VTK: 1.0
   ChimeraX-WavefrontOBJ: 1.0
   ChimeraX-WebCam: 1.0
   ChimeraX-WebServices: 1.0
   ChimeraX-Zone: 1.0
   colorama: 0.4.4
   comtypes: 1.1.10
   cxservices: 1.1
   cycler: 0.10.0
   Cython: 0.29.24
   decorator: 5.1.0
   docutils: 0.17.1
   filelock: 3.0.12
   funcparserlib: 0.3.6
   grako: 3.16.5
   h5py: 3.5.0
   html2text: 2020.1.16
   idna: 3.3
   ihm: 0.21
   imagecodecs: 2021.4.28
   imagesize: 1.2.0
   ipykernel: 5.5.5
   ipython: 7.23.1
   ipython-genutils: 0.2.0
   jedi: 0.18.0
   Jinja2: 3.0.1
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   kiwisolver: 1.3.2
   lxml: 4.6.3
   lz4: 3.1.3
   MarkupSafe: 2.0.1
   matplotlib: 3.4.3
   matplotlib-inline: 0.1.3
   msgpack: 1.0.2
   netCDF4: 1.5.7
   networkx: 2.6.3
   numexpr: 2.7.3
   numpy: 1.21.2
   openvr: 1.16.801
   packaging: 21.0
   ParmEd: 3.2.0
   parso: 0.8.2
   pickleshare: 0.7.5
   Pillow: 8.3.2
   pip: 21.2.4
   pkginfo: 1.7.1
   prompt-toolkit: 3.0.21
   psutil: 5.8.0
   pycollada: 0.7.1
   pydicom: 2.1.2
   Pygments: 2.10.0
   PyOpenGL: 3.1.5
   PyOpenGL-accelerate: 3.1.5
   pyparsing: 3.0.3
   PyQt5-commercial: 5.15.2
   PyQt5-sip: 12.8.1
   PyQtWebEngine-commercial: 5.15.2
   python-dateutil: 2.8.2
   pytz: 2021.3
   pywin32: 228
   pyzmq: 22.3.0
   qtconsole: 5.1.1
   QtPy: 1.11.2
   RandomWords: 0.3.0
   requests: 2.26.0
   scipy: 1.7.1
   Send2Trash: 1.8.0
   SEQCROW: 1.3
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   sphinxcontrib-devhelp: 1.0.2
   sphinxcontrib-htmlhelp: 2.0.0
   sphinxcontrib-jsmath: 1.0.1
   sphinxcontrib-qthelp: 1.0.3
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   suds-jurko: 0.6
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   wheel-filename: 1.3.0
   WMI: 1.5.1